102 research outputs found
Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
BACKGROUND: Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. RESULTS: These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. CONCLUSION: These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth
Citizen-Science for the Future: Advisory Case Studies From Around the Globe
The democratization of ocean observation has the potential to add millions of observations every day. Though not a solution for all ocean monitoring needs, citizen scientists offer compelling examples showcasing their ability to augment and enhance traditional research and monitoring. Information they are providing is increasing the spatial and temporal frequency and duration of sampling, reducing time and labor costs for academic and government monitoring programs, providing hands-on STEM learning related to real-world issues and increasing public awareness and support for the scientific process. Examples provided here demonstrate the wide range of people who are already dramatically reducing gaps in our global observing network while at the same time providing unique opportunities to meaningfully engage in ocean observing and the research and conservation it supports. While there are still challenges to overcome before widespread inclusion in projects requiring scientific rigor, the growing organization of international citizen science associations is helping to reduce barriers. The case studies described support the idea that citizen scientists should be part of an effective global strategy for a sustained, multidisciplinary and integrated observing system
Global biogeography of SAR11 marine bacteria
The ubiquitous SAR11 bacterial clade is the most abundant type of organism in the worldĝ€™s oceans, but the reasons for its success are not fully elucidated. We analysed 128 surface marine metagenomes, including 37 new Antarctic metagenomes. The large size of the data set enabled internal transcribed spacer (ITS) regions to be obtained from the Southern polar region, enabling the first global characterization of the distribution of SAR11, from waters spanning temperatures ĝ̂'2 to 30°C. Our data show a stable co-occurrence of phylotypes within both ĝ€̃ tropicalĝ€™ (>20°C) and ĝ€̃ polarĝ€™ (<10°C) biomes, highlighting ecological niche differentiation between major SAR11 subgroups. All phylotypes display transitions in abundance that are strongly correlated with temperature and latitude. By assembling SAR11 genomes from Antarctic metagenome data, we identified specific genes, biases in gene functions and signatures of positive selection in the genomes of the polar SAR11ĝ€"genomic signatures of adaptive radiation. Our data demonstrate the importance of adaptive radiation in the organismĝ€™s ability to proliferate throughout the worldĝ€™s oceans, and describe genomic traits characteristic of different phylotypes in specific marine biomes. © 2012 EMBO and Macmillan Publishers Limited All rights reserved
Modeling the cosmological co-evolution of supermassive black holes and galaxies: I. BH scaling relations and the AGN luminosity function
We model the cosmological co-evolution of galaxies and their central
supermassive black holes (BHs) within a semi-analytical framework developed on
the outputs of the Millennium Simulation. This model, described in detail in
Croton et al. (2006) and De Lucia & Blaizot (2007), introduces a `radio mode'
feedback from Active Galactic Nuclei (AGN) at the centre of X-ray emitting
atmospheres in galaxy groups and clusters. Thanks to this mechanism, the model
can simultaneously explain: (i) the low observed mass drop-out rate in cooling
flows; (ii) the exponential cut-off in the bright end of the galaxy luminosity
function; and (iii) the bulge-dominated morphologies and old stellar ages of
the most massive galaxies in clusters. This paper is the first of a series in
which we investigate how well this model can also reproduce the physical
properties of BHs and AGN. Here we analyze the scaling relations, the
fundamental plane and the mass function of BHs, and compare them with the most
recent observational data. Moreover, we extend the semi-analytic model to
follow the evolution of the BH mass accretion and its conversion into
radiation, and compare the derived AGN bolometric luminosity function with the
observed one. While we find for the most part a very good agreement between
predicted and observed BH properties, the semi-analytic model underestimates
the number density of luminous AGN at high redshifts, independently of the
adopted Eddington factor and accretion efficiency. However, an agreement with
the observations is possible within the framework of our model, provided it is
assumed that the cold gas fraction accreted by BHs at high redshifts is larger
than at low redshifts.Comment: 15 pages, 7 figures, MNRAS submitte
Modeling the cosmological co-evolution of supermassive black holes and galaxies: II. The clustering of quasars and their dark environment
We use semi-analytic modeling on top of the Millennium simulation to study
the joint formation of galaxies and their embedded supermassive black holes.
Our goal is to test scenarios in which black hole accretion and quasar
activity are triggered by galaxy mergers, and to constrain different models for
the lightcurves associated with individual quasar events. In the present work
we focus on studying the spatial distribution of simulated quasars. At all
luminosities, we find that the simulated quasar two-point correlation function
is fit well by a single power-law in the range 0.5 < r < 20 h^{-1} Mpc, but its
normalization is a strong function of redshift. When we select only quasars
with luminosities within the range typically accessible by today's quasar
surveys, their clustering strength depends only weakly on luminosity, in
agreement with observations. This holds independently of the assumed lightcurve
model, since bright quasars are black holes accreting close to the Eddington
limit, and are hosted by dark matter haloes with a narrow mass range of a few
10^12 h^{-1} M_sun. Therefore the clustering of bright quasars cannot be used
to disentangle lightcurve models, but such a discrimination would become
possible if the observational samples can be pushed to significantly fainter
limits.
Overall, our clustering results for the simulated quasar population agree
rather well with observations, lending support to the conjecture that galaxy
mergers could be the main physical process responsible for triggering black
hole accretion and quasar activity.Comment: 17 pages, 16 figures, to be published on MNRA
The ocean sampling day consortium
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean
Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, freeliving bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages. comparative genomics | marine microbiology | microbial ecology | microbial microevolution | operational taxonomic uni
The Ocean Sampling Day Consortium
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
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